San Francisco has the better airport, by far. It also has BART train service directly from the International Terminal to the city and other parts of the Bay Area. September is a great time for California (I like late in the month best) because it's cooler and less crowded with tourists, but because of the great weather the exception will be San Francisco itself (make sure you have reservations in SF as they can be hard to come by at that time).

A car in downtown SF can be more of a problem than an advantage - extremely high parking fees, and a car is a very poor way to see the city anyway. This city is tiny, and the best way to see it is on foot, bike or cable car. LA is just the opposite because it's so spread out.